The biomineralization process and skeletal growth dynamics of azooxanthellate corals are poorly known. Here, the growth rate of the shallow-water dendrophyllid scleractinian coral Balanophyllia regia was evaluated with calcein-labeling experiments that showed higher lateral than vertical extension. The structure, mineralogy and trace element composition of the skeleton were characterized at high spatial resolution. The epitheca and basal floor had the same ultrastructural organization as septa, indicating a common biological control over their formation. In all of these aragonitic skeletal structures, two main ultrastructural components were present: "centers of calcification" (COC) also called rapid accretion deposits (RAD) and "fibers" (thickening deposits, TD). Heterogeneity in the trace element composition, i.e., the Sr/Ca and Mg/Ca ratios, was correlated with the ultrastructural organization: magnesium was enriched by a factor three in the rapid accretion deposits compared with the thickening deposits. At the interface with the skeleton, the skeletogenic tissue (calicoblastic epithelium) was characterized by heterogeneity of cell types, with chromophile cells distributed in clusters regularly spaced between calicoblasts. Cytoplasmic extensions at the apical surface of the calicoblastic epithelium created a three-dimensional organization that could be related to the skeletal surface microarchitecture. Combined measurements of growth rate and skeletal ultrastructural increments suggest that azooxanthellate shallow-water corals produce well-defined daily growth steps.